What I want to do is create a custom template under the "My templates..." section of the HTML files portion of Developer Studio.

What I would like to do is have a pre-determined layout with our logo and a custom CSS file already linked to it. How do I go about doing this?

I am on 7703

The "My Templates" area is not supported currently. You would need to use appl.css for your overrides and check the box to apply appl.css.